Development of Sequence Characterized Amplified Region (SCAR) Primers for the Detection of Resistance to Sporisorium reiliana in Maize

AbstractRandom amplified polymorphic DNA (RAPD) analyses were performed with random primer H16 for the B biotype and two non-B populations of Bemisia tabaci collected from Zhejiang (China). The specific sequence fragments containing 446, 390 and 1317 nucleotides were amplified for the B biotype, ZHJ-1, ZHJ-2 populations, respectively. The three specific fragments were cloned and sequenced, and three pairs of SCAR primers were designed according to the sequences determined. With improvement of the conditions of the polymerase chain reaction (PCR), the specific fragments of B biotype, ZHJ-1 and ZHJ-2 populations, namely 439, 366 and 1238 nucleotides, respectively, were amplified with the sequence characterized amplified region (SCAR) primer of the corresponding population, while specific fragments of the other populations of B. tabaci or Trialeurodes vaporariorum could not be amplified.

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Development of SCAR markers for sex determination in the dioecious shrub Aucuba japonica (Cornaceae)

Genome ◽

10.1139/g08-120 ◽

2009 ◽

Vol 52 (3) ◽

pp. 231-237 ◽

Cited By ~ 12

Author(s):

Masayuki Maki

Keyword(s):

Sex Identification ◽

The Other ◽

Scar Markers ◽

Specific Sequence ◽

Sequence Characterized Amplified Region ◽

Annealing Temperatures ◽

Aucuba Japonica ◽

Males And Females ◽

Male Specific ◽

Scar Primers

Two sex-linked fragments were identified by RAPD analyses in the dioecious diploid shrub Aucuba japonica var. ovoidea and were converted into markers of male-specific sequence characterized amplified region (SCAR) markers. PCRs using the primers designed in this study correctly discriminated 24 flowering males and 24 flowering females at higher annealing temperatures (SCAR markers OPA10-424 at 55 °C and OPN11-1095 at 65 °C), although at relatively low annealing temperatures, the fragments were amplified in both males and females. These SCAR primers were also tested to see whether they were applicable to sex identification in the conspecific tetraploid Aucuba japonica var. japonica. One set pf SCAR primers could be used for sex identification even in this tetraploid variety, although the other failed. The SCAR markers developed in this study will provide a powerful tool in identifying the sex of immature plants of dioecious A. japonica, which is a commercially valuable shrub due to its conspicuous fruits.

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Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species

Genome ◽

10.1139/g02-054 ◽

2002 ◽

Vol 45 (5) ◽

pp. 862-870 ◽

Cited By ~ 90

Author(s):

Onivaldo Randig ◽

Michel Bongiovanni ◽

Regina M.D.G Carneiro ◽

Philippe Castagnone-Sereno

Keyword(s):

Genetic Diversity ◽

Multiplex Pcr ◽

Rapd Markers ◽

Phylogenetic Analyses ◽

The Other ◽

Scar Markers ◽

Meloidogyne Hapla ◽

Root Knot Nematodes ◽

Sequence Characterized Amplified Region ◽

Scar Primers

RAPD markers were used to characterize the genetic diversity and relationships of root-knot nematodes (RKN) (Meloidogyne spp.) in Brazil. A high level of infraspecific polymorphism was detected in Meloidogyne arenaria, Meloidogyne exigua, and Meloidogyne hapla compared with the other species tested. Phylogenetic analyses showed that M. hapla and M. exigua are more closely related to one another than they are to the other species, and illustrated the early divergence of these meiotically reproducing species from the mitotic ones. To develop a PCR-based assay to specifically identify RKN associated with coffee, three RAPD markers were further transformed into sequence-characterized amplified region (SCAR) markers specific for M. exigua, Meloigogyne incognita and Meloidogyne paranaensis, respectively. After PCR using the SCAR primers, the initial polymorphism was retained as the presence or absence of amplification. Moreover, multiplex PCR using the three pairs of SCAR primers in a single reaction enabled the unambiguous identification of each species, even in mixtures. Therefore, it is concluded that the method developed here has potential for application in routine diagnostic procedures.Key words: diagnostic, multiplex PCR, phylogeny, RAPD, root-knot nematodes.

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Eastern Filbert Blight-resistant Hazelnuts from Russia, Ukraine, and Poland

HortScience ◽

10.21273/hortsci.48.4.466 ◽

2013 ◽

Vol 48 (4) ◽

pp. 466-473 ◽

Cited By ~ 10

Author(s):

John M. Capik ◽

Megan Muehlbauer ◽

Ari Novy ◽

Josh A. Honig ◽

Thomas J. Molnar

Keyword(s):

Genetic Resistance ◽

Corylus Avellana ◽

Eastern North America ◽

Sources Of Resistance ◽

Sequence Characterized Amplified Region ◽

Disease Phenotypes ◽

Anisogramma Anomala ◽

The Russian Federation ◽

Eastern Filbert Blight ◽

Scar Primers

Stable genetic resistance to the fungal disease eastern filbert blight (EFB), caused by Anisogramma anomala, is vital for sustainable production of European hazelnut (Corylus avellana) in eastern North America. In this study, new hazelnut germplasm from the Russian Federation, Ukraine, and Poland (a total of 1844 trees from 66 seed lots) was subjected to A. anomala under field conditions over at least five years in New Jersey. Plants were then rated for the presence of EFB using an index of 0 (no disease) through 5 (all stems containing cankers). Nuts of the resistant trees were evaluated to identify plants with improved kernel characteristics. Genomic DNA of these trees was also screened with sequence-characterized amplified region (SCAR) markers generated by the primers BE-03, BE-33, and BE-68, which are closely linked to the single dominant R-gene of ‘Gasaway’, to assess the resistant seedlings for the presence of this well-known source of resistance. At final evaluation, 76 trees remained free of disease with nine expressing only minor symptoms (rating 1 or 2). The resistant trees spanned 24 different seed lots representing all three countries. The remaining trees ranged from moderately to severely infected with 81% of the total collection rating 5. Several of the resistant trees were found to produce commercial-sized (≈12 mm diameter), round kernels that blanched well. Although the results of the ‘Gasaway’ SCAR primers were inconclusive, the diverse collection origins and disease phenotypes provide evidence that novel sources of resistance were likely identified in this study. These new plants should broaden the genetic base of EFB-resistant C. avellana hazelnut germplasm available for breeding.

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Sequence-characterized amplified region (SCAR) technique used for variety discrimination in vinca (Catharanthus roseus (L.) G.Don)

Revista Brasileira de Sementes ◽

10.1590/s0101-31222002000100041 ◽

2002 ◽

Vol 24 (1) ◽

pp. 299-305 ◽

Cited By ~ 1

Author(s):

Carlos C.E Menezes ◽

Tara Vantoai ◽

Miller B McDonald ◽

Tocio Sediyama

Keyword(s):

Catharanthus Roseus ◽

Seed Quality ◽

Sequence Information ◽

Genetic Purity ◽

Banding Patterns ◽

Sequence Characterized Amplified Region ◽

Purity Testing ◽

Polymorphic Bands ◽

Scar Primers

Sequence-Characterized Amplified Region (SCAR) appears as a useful technique for genetic purity testing and variety discrimination, applicable to species in which some other techniques have failed. In particular, this technique is very attractive with species in which RAPD results were not consistent. The RAPD polymorphic bands were cloned, sequenced and from the sequence information, primers pairs for normal PCR were developed. Since the probability of obtaining successful SCAR primers from RAPD polymorphic bands was about 50%, a larger number of RAPD polymorphic bands are needed to develop sufficient SCAR primers for varietal discrimination in vinca. In addition, the efficiency of the SCAR technique is strongly affected by the quality of DNA extracted from seeds. The SCAR banding patterns obtained from vinca seed were consistent and repeatable making the results reliable for genetic purity testing and variety discrimination. The SCAR technique is simple, fast, relatively inexpensive and allows the use of DNA extracted from dry seeds, which is very important in a seed-quality evaluating program

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Development of Randomly Amplified Polymorphic DNA Based SCAR Marker for Identification ofIpomoea mauritianaJacq (Convolvulaceae)

Evidence-based Complementary and Alternative Medicine ◽

10.1093/ecam/neq023 ◽

2011 ◽

Vol 2011 ◽

pp. 1-6 ◽

Cited By ~ 7

Author(s):

Kambiranda Devaiah ◽

Subramani Paranthaman Balasubramani ◽

Padma Venkatasubramanian

Keyword(s):

Scar Marker ◽

The Other ◽

Herbal Drug ◽

Randomly Amplified Polymorphic Dna ◽

Pueraria Tuberosa ◽

Sequence Characterized Amplified Region ◽

Cycas Circinalis ◽

Scar Primers

Vidari is an Ayurvedic herbal drug used as aphrodisiac, galactagogue and is also used in the preparation ofChyavanaprash. Tubers ofIpomoea mauritianaJacq. (Convolvulaceae),Pueraria tuberosa(Roxb. ex Willd.) DC (Fabaceae),Adenia hondala(Gaertn.) de Wilde (Passifloraceae) and pith ofCycas circinalisL. (Cycadaceae) are all traded in the name of Vidari, creating issues of botanical authenticity of the Ayurvedic raw drug. DNA-based markers have been developed to distinguishI. mauritianafrom the other Vidari candidates. A putative 600-bp polymorphic sequence, specific toI. mauritianawas identified using randomly amplified polymorphic DNA (RAPD) technique. Furthermore, sequence characterized amplified region (SCAR) primers (IM1F and IM1R) were designed from the unique RAPD amplicon. The SCAR primers produced a specific 323-bp amplicon in authenticI. mauritianaand not in the allied species.

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Seleksi Marka SCAR untuk Identifikasi Dini Jenis Kelamin Tanaman Pepaya (The Selection of SCAR Markers for Early Sex Identification of Papaya)

Jurnal Hortikultura ◽

10.21082/jhort.v30n1.2020.p1-8 ◽

2020 ◽

Vol 30 (1) ◽

pp. 1

Author(s):

NFN Noflindawati ◽

Aswaldi Anwar ◽

Agus Sutanto ◽

NFN Yusniwati

Keyword(s):

Sex Expression ◽

Scar Markers ◽

Tropical Fruit ◽

Sequence Characterization ◽

Sequence Characterized Amplified Region ◽

Plant Sex ◽

Scar Primers ◽

Selection Of ◽

Physiological Characters

Identifikasi dini terhadap jenis kelamin tanaman pepaya merupakan hal penting yang dapat membantu petani dalam budidaya tanaman pepaya. Identifikasi kelamin pepaya berdasarkan marka morfologi dan fisiologi telah dilakukan, namun beberapa hasilnya masih bias karena faktor lingkungan. Identifikasi kelamin tanaman pepaya menggunakan marka molekuler bisa lebih cepat dan akurat. Penelitian tersebut telah banyak dilakukan, salah satu di antaranya adalah marka berbasis sequence characterized amplified region (SCAR) dan beberapa primer SCAR telah dihasilkan untuk identifikasi kelamin pepaya. Penelitian bertujuan untuk menyeleksi primer SCAR yang efektif dalam mengidentifikasi seks tanaman pepaya. Penelitian dilakukan pada bulan November 2018 sampai Juni 2019 di Laboratorium Molekuler dan Uji Mutu Kebun Percobaan Sumani Balai Penelitian Tanaman Buah Tropika di Solok. Primer SCAR yang diseleksi adalah W11,T12, PKBT5, Napf2, dan SDp. Tanaman referensi sebagai sampel umur 11–12 bulan adalah tanaman betina, jantan, dan hermaprodit masing-masing lima tanaman dari pepaya lokal dan Merah Delima. Hasil penelitian menunjukkan bahwa lima primer SCAR yang diuji hanya dapat membedakan tanaman betina dengan tanaman jantan dan hermaprodit tetapi belum dapat membedakan antara tanaman jantan dengan hermaprodit. Konsistensi pola amplifikasi dihasilkan dari primer SCAR W11, Napf2, dan T12 dengan posisi 800 bp. Primer SCAR W11, Napf2, dan T12 selanjutnya dapat digunakan sebagai marka untuk identifikasi kelamin tanaman betina dengan tanaman jantan dan hermaprodit.KeywordsSCAR; Identifikasi; Pepaya; Jantan, Hermaprodit AbstractThe determination of sex expression of papaya plants is important to farmers in its cultivation. The identification of papaya plant sex based on morphological and physiological characters have been previously carried out, however, the results were still biased due to environmental factors. Many studies have been carried out to identify this plant sex, such as the use of molecular and SCAR markers, based on sequence characterization on amplified regions. This research aims to select the SCAR primers that are effective in identifying papaya plant sex. The study was conducted from November 2018 to June 2019, at Laboratory of Molecular and Quality Testing of the Indonesian Tropical Fruit Research Institute in Solok. The selected SCAR primers were W11, T12, PKBT5, Napf2, and SDp, using a total of five female, male, and hermaphrodite plants are reference aged 11–12 month from local papaya and cv. Merah Delima. The five SCAR primers tested were only able to differentiate females from male and hermaphrodite plants. The consistency of the amplification pattern was obtained from the SCAR W11, T12, and Napf2 primers at 800 bp. In conclusion, SCAR W11, Napf2, and T12 primers are used as markers to distinguish female plants from male and hermaphrodite.

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Evaluation of SCAR Markers to Identify Raspberry Cultivars

HortScience ◽

10.21273/hortsci.30.4.856b ◽

1995 ◽

Vol 30 (4) ◽

pp. 856B-856 ◽

Cited By ~ 2

Author(s):

Jean-Guy Parent ◽

Daniele Page

Keyword(s):

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Pcr Primers ◽

Sequence Information ◽

Scar Markers ◽

Certification Program ◽

Reaction Conditions ◽

Sequence Characterized Amplified Region ◽

Sequence Method ◽

Scar Primers

Random amplified polymorphic DNA (RAPD) markers are used in Quebec's certification program to verify the identity of raspberry cultivars. However, sequence characterized amplified region (SCAR) markers, less sensitive to modifications in reaction conditions, could be derived from RAPD markers. Our objective was to evaluate the potential of SCAR markers to replace the RAPD ones. Five RAPD markers obtained with primer OPG06 (length of 520, 700, 825, 1450, and 2000 bp) were cloned in pTZ/PC or pCRII vectors. Extremities of the cloned markers were sequenced by the nonradioactive silver sequence method using pUC/M13 forward and reverse primers. Sequence information was used to make SCAR primers, similar in length to standard PCR primers. Some SCAR primers were elongated RAPD primers, whereas others were from internal regions. Ability of primer pairs and combination of primer pairs to discriminate cultivars of our certification program was compared with their RAPD counterparts as well as with the technical feasibility of both methods.

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Conversion of sequence-characterized amplified region (SCAR) bands into high-throughput DNA markers based on RAPD technique for detection of the stem nematode Ditylenchus dipsaci in crucial plant hosts

Plant Soil and Environment ◽

10.17221/2226-pse ◽

2008 ◽

Vol 53 (No. 3) ◽

pp. 97-104 ◽

Cited By ~ 12

Author(s):

M. Zouhar ◽

M. Marek ◽

O. Douda ◽

J. Mazáková ◽

P. Ryšánek

Keyword(s):

Cost Effective ◽

Healthy Plant ◽

Host Preferences ◽

Sequence Characterized Amplified Region ◽

Detection And Identification ◽

Plant Hosts ◽

Cost Effective Technique ◽

Ditylenchus Dipsaci ◽

Species Specific ◽

Template Dna

Ditylenchus dipsaci, the stem nematode, is a migratory endoparasite of over 500 species of angiosperms. The main method of D. dipsaci control is crop rotation, but the presence of morphologically indistinguishable host races with different host preferences makes rotation generally ineffective. Therefore, a sensitive, rapid, reliable, as well as cost effective technique is needed for identification of D. dipsaci in biological samples. This study describes the development of species-specific pairs of PCR oligonucleotides for detection and identification of the D. dipsaci stem nematode in various plant hosts. Designed DIT-2 primer pair specifically amplified a fragment of 325 bp, while DIT-5 primer pair always produced a fragment of 245 bp in all D. dipsaci isolates. Two developed SCAR primer pairs were further tested using template DNA extracted from a collection of twelve healthy plant hosts; no amplification was however observed. The developed PCR protocol has proved to be quite sensitive and able to specifically detect D. dipsaci in artificially infested plant tissues.

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